- Dönitz, Jürgen, and Edgar Wingender. "The ontology-based answers (OBA) service: A connector for embedded usage of ontologies in applications." Frontiers in Genetics 3: 197.
Our recent OntoCAT paper has just reached the list of top 10 most most viewed articles in BMC Bioinformatics this month:
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OntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies.
OntoCAT exists in many flavours including a stand-alone database and browser, REST service, Google App application and ontoCAT R package to work with ontologies in R environment. See download page for all the options.
The current repertoire of supported ontology resources can easily be extended for other resources. Such services would only need to implement the OntologyService interface to immediately become aligned with pre-existing resources and allow for their seamless interchangeability.
Releases are often and tested nightly, so that you never have to worry about the updates in the underlying resources.
OntoCAT is open source and available under the LGPLv3 license.
How to cite us
Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson and Morris A. Swertz BMC Bioinformatics 2011, 12:218
Article | BibTeX
ontoCAT: an R package for ontology traversal and search
Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M. Bioinformatics. 2011 Jun 22.
Posters & talks
[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks, The 12th Annual Bioinformatics Open Source Conference (BOSC 2011), co-located with ISMB/ECCB 2011, Vienna, Austria. Slides available from http://slidesha.re/mXlCVl
Adamusiak Tomasz, Burdett Tony, van der Velde K Joeri, Abeygunawardena Niran, Antonakaki Despoina, Parkinson Helen, and Swertz Morris. OntoCAT – a simpler way to access ontology resources. Available from Nature Precedings < http://dx.doi.org/10.1038/npre.2010.4666.1> (2010)
Tomasz Adamusiak <tomasz@…>
Morris Swertz <m.a.swertz@…>
Natalja Kurbatova <natalja@…>
OntoCAT has been developed in the framework of the European Commission's Seventh Framework Programme GEN2PHEN project (grant number 226073), which aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data. The GEN2PHEN Consortium members have been selected from a talented pool of European research groups and companies that are interested in the G2P database challenge. Additionally, a few non-EU participants have been included to bring extra capabilities to the initiative.
This work was also supported by the FP7 Programmes: SLING (grant number 226073), and SYBARIS (grant number 242220), the European Molecular Biology Laboratory, the Netherlands Organisation for Scientific Research (NWO/Rubicon grant number 825.09.008), and the Netherlands Bioinformatics Centre (BioAssist/Biobanking platform and BioRange grant SP1.2.3).
OntoCAT's development is a joint effort between the Functional Genomics Group at the European Informatics Institute, UK and the Genomics Coordination Center, University Medical Center Groningen, the Netherlands.
Special thanks go to NCBO BioPortal and EBI OLS support teams for all the comprehensive help they provide.
OntoCAT logo courtesy of Eamonn Maguire.